On 10/20/19 5:57 AM, Olga Press wrote:
Prof. Lemkul, Thank you very much for your reply. I would be very grateful if you can help me with some questions regarding voids compression. Should I run the NPT equilibration on the whole system( including protein+membrame+solvent +*ions*) meaning, should I continue my protocol (adding ions-->NVT equilibration with position restraints on the protein---> and than NPT equilibration with position restraints---> NPT equilibration without restraints) or should I run first NPT equilibration without position restraints (and for how long?) and than continue the protocol?
A normal protocol with restraints on your protein should work fine. Those voids will be gone within tens of picoseconds.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
